So it's still an App Store bug, that it goes past the Startup drive. It should really only be looking at System and Application folders.

Just because something doesn't work the way you think it should doesn't mean it's a bug.

Consider the question: What should an updater do if it finds more than one copy of the app it's supposed to update?

Answering a question like this is one reason why it's so hard for software designers to provide a good user experience.

It seems like a simpler question, but I don't think there is a simple correct answer.

Apple's updater updates all copies it finds, which you dislike.

But if instead it only updated the copy on the boot drive, some users will complain that it didn't update all their copies.

Microsoft's updater has an interesting solution: If it's trying to update Word, and it finds multiple copies, it asks you which one you want to update.

But as I recall, it lists them alphabetically according to path name. So if your boot drive is called "Macintosh HD," and your backup drive is called "Backup drive," the wrong one gets listed first.

And what if you want to update all of your copies of Word? That's not even an option. In that case, you'd have to run the updater multiple times to get all your copies updated.

I don't reboot for weeks at a time…

As I type this, it's been 27 days 6 hours, and 24 minutes since I last rebooted.

But my advice still stands. I use SuperDuper!, which can be scheduled to to auto-mount the backup driver, clone to the boot drive to the backup, and auto-unmount it when done.

Which means my backup drive is only ever mounted during a clone operation. The exception is on those occasions when I first boot up. Since I do it so rarely, I just manually eject my clone. But when I set this up for a client, I use an AppleScript set as a startup item to auto-unmount it,.

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